I have noticed this problem too -_-. Here listen to this newegg review:
"The front panel audio ports make horrible static/computer noise rendering them useless. This is not because of bad cable shielding, this is due to the fact that the USB ports and audio jacks share a ground connection. All of the front panel ports are encased in a solid plastic block, so there's no way to separate the grounds. However, I did find a partial solution. see other thoughts...
Other Thoughts: By disconnecting the usb ground wires from the motherboard (just un-clip the black wires out of the black usb plug that goes into the motherboard) and the ground wire above the cd drive bay; all of the noise is eliminated, until you plug in a usb device. A usb device plugged into the front ports makes for some horrible noise (dialup modemish). So unplug your headphones when using front panel usb (or enjoy the sound of USB), and you will never have a problem.
the esata, usb, and audio ports on the front panel should not share a common ground between them. Each device should use it's own ground connection back to the motherboard. Multiple ground paths make for a noisy ride...
I would be a very happy person if Antec could just mail out a front panel module that was fixed."
I personally have not tried this because i don't want to risk shocking anything that isn't grounded, so i just deal with it; you can't really hear it anyways once music is playing or you're in a game.